Terms for bryophytes and ferns are not linked to any ontology

[baskaufs]

Currently, the definitions given for bryophyte and fern parts are those suggested by Mervin Perez. However, for nearly all of the other CV terms in the Views vocabularies, the definitions were taken from ontologies, and linked to those ontology IRIs. We need to add these, or decide it isn't possible. See the terms at the bottom of https://github.com/tdwg/ac/blob/master/views/code/subjectPart/subjectPart_cv.csv

[nielsklazenga]

I happen to be a bryologist and would love to work on an ontology of bryophyte structures, when I can find the time.

At the moment I do not actually see any terms that are particularly relevant to bryophytes in the list. archegoniophore, antheridiophore and gemmae cups only occur in a small group of liverworts. They would definitely be in an ontology of bryophyte structures, so are unproblematic, but will just not be used very often.

gametophyte and sporophyte, on the other hand, in bryology, are (or should be) strictly used for the generations, between sporogenesis and gametogenesis and between gametogenesis and sporogenesis respectively; the respective structures are called gametophore (which does not include the protonema) and sporogone (sporophore is used in mycology). Sporophyte, as a structure, is used in pteridology, but the 'remaining attached to the gametophyte and partially dependent on it' seems to be targeting bryophytes in particular (but that might be my lack of understanding of ferns).

[baskaufs]

We generally have attempted defining values for parts that are too granular. However, in the case of archegoniophore, antheridiophore and gemmae cups, the issue is that they occur in a narrow group of organisms rather than that they are a very detailed level of structure. We are missing parts for many "narrow" groups of organisms, but that's generally because we didn't have any participants in the process to tell us what those parts should be. In this case we actually did have someone who identified them as relevant for us. So I don't necessarily think there is harm in keeping them, although if we do, we should correctly define them and also clarify the group of organisms for which they are relevant.

[baskaufs]

@nielsklazenga Would it fix things if we changed the label from "sporophyte" to "sporogone"?

Although we have created terms for bryophytes and ferns, I don't think we have actually tested them thoroughly. I will make a suggestion. Here is a page with a variety of images of non-seed plants: http://bioimages.vanderbilt.edu/pages/non-seed-plants.htm . I would suggest we make it an exercise to apply subjectPart and subjectOrientation values to each of them. If we can successfully do that, then it might be reasonable to conclude that the controlled values we have will work. If we cannot, then perhaps we need to abandon the attempt to add these to the initial vocabulary and hope to add them later when they can be better worked out.

If one or more people would like to take the time to do this, I've created a Google Sheet with all of the image URLs on it. You can make a copy of it and fill in the subjectPart and subjectOrientation values. If you need access to the sheet, email me at steve.baskauf@vanderbilt.edu and I'll grant it.

[baskaufs]

Sorry, I forgot the link to the Google sheet: https://docs.google.com/spreadsheets/d/1onX9qnwfcSWM5rxt2b-8A7oLx2xBPG09QPZUzyKJCso/edit?usp=sharing

[afuchs1]

Hi, sorry for contributing later to this conversation. In our image database we use the following attributes for categorising the bryophyte parts in the image.
GAMETOPHYTE
SPOROPHYTE
SPORE
SPORANGIA
THALLUS
FRUITING_BODY

[baskaufs]

Due to lack of consensus and testing prior to completion of implementation experience testing, these proposed terms were removed from the vocabularies and documented as future candidate terms in b54222a